SUPER-FOCUS outcome result

[song...@gmail.com]

Hello

I just used the SUPER-FOCUS program to analyze my metagenome libraries. I noticed that the outcome file doesn't list which sequence ID matches with annotated gene/enzymes and metabolisms. Is there a way to obtain this info.

Thank you.

BK Song

[Geni]

Hi Dr. Song, 

If you want to know which sequence aligned to a subsystem, you need to fun the tool using the parameter -k 1, so it keeps the original alignment and you can look into it. 

[song...@gmail.com]

Thanks for the response.

I have another question regarding the use of Super-focus program. I made an amplicon library of nitrite reductase genes (nirS) and ran the super-focus to find out the closest matching taxa of each nirS sequence. I got a list of taxa for each sequence, which made the output file too large and failed to generate an annotation summary file. Is there a way to list the first top matching taxa only in the output file?

[Geni]

Song,
SUPER-FOCUS uses FOCUS for the taxa annotation, and FOCUS was not designed for amplicons, so I would not trust the taxa profile. On the other hand, you should be fine with the functional profiling.

Best